Efficient calculation of exact mass isotopic distributions

Snider, Ross

doi:10.1016/j.jasms.2007.05.016

Cited by 35 publications

(46 citation statements)

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“…C 63 H 100 N 18 O 13 S has 51,582,720 individual isotopic species spread across 212 levels, and it only takes about 40 min for our algorithm to generate the whole isotopic distribution on Intel Core2 Duo CPU@2.0GHz machine with 2 gigabytes of RAM. As a comparison, the latest published isoDalton program [20] ran out of memory on the same machine (isoDalton was downloaded from MATLAB Central File Exchange that was submitted on 07/30/2007, http://www.mathworks. com/matlabcentral/fileexchange/loadFile.do?objectId ϭ 15,752).…”

Section: Resultsmentioning

confidence: 99%

“…Based on this polynomial representation, many stepwise calculation methods [15][16][17][18][19][20] have been proposed. All of these polynomial-based methods could theoretically compute the exact isotopic distribution of any molecule, i.e., "infinite" resolution, but fail for large molecules in practice because the number of isotopic species of a large molecule could be immense (due to combinatorial explosion with the increase of molecule weight To calculate the exact mass and the exact abundance of every isotopic species of a molecule, polynomial-based methods need to keep all isotopic species of the molecule in memory simultaneously.…”

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confidence: 99%

“…For example, more than 4000 gigabytes of RAM are required to compute the isotopic distribution of bovine insulin. To deal with the memory problem, stepwise methods used the pruning technique [15] each time an atom [20] or an element [15] or a hypothetical atom cluster [19] is added to only keep those isotopic species with abundances above a user defined threshold. Therefore, a direct consequence of pruning is that some species are missing.…”

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A hierarchical algorithm for calculating the isotopic fine structures of molecules

Kresh

Karabacak

et al. 2008

J. Am. Soc. Mass Spectrom.

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This article presents a memory efficient algorithm for accurately calculating the isotopic fine structures of molecules. Treating individual isotopic species of a molecule as different mass states, we introduce the concept of transitions between mass states and represent all mass states of the molecule in a hierarchical structure. We show that there exists a simple relationship between two different mass states at two different levels of the hierarchical structure. This allows us to efficiently and accurately compute both the mass and the abundance of every mass state of a small to medium-sized molecule, whose gross structures include small number of fine structures. A truncated calculation of this algorithm can be applied to calculate a majority of isotopic species (99.99% of cumulative abundance) of a large

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A hierarchical algorithm for calculating the isotopic fine structures of molecules

Kresh

Karabacak

et al. 2008

J. Am. Soc. Mass Spectrom.

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“…We mistakenly assumed that the NIST [2] values used by IsoDalton [3] were identical to the IUPAC 1997 standard (Table 1). However, this confusion did not influence the comparison between BRAIN and the other methods reported in our paper, as all the abundances and masses in our comparison were changed to the values used by IsoDalton [3].…”

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confidence: 99%

“…For larger fluctuations of the masses and/or abundances of elemental isotopes, the effect on the isotopic distribution is even more pronounced and, in some cases, becomes troubling, as illustrated in Tables 2 and 3. The tables show the differences between the theoretical monoisotopic masses (Equation 24 in [1]) and theoretical average masses (Equation 25 in [1]) of 10 molecules [1] based upon the default isotope information used by BRAIN [1] and IsoDalton [3] (NIST), the IUPAC1997 standard [4], IsoPro [5], Mercury [6] and Emass [7], and NeutronCluster [8] (Table S1 in [1]). …”

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Claesen

Dittwald

Burzykowski

et al. 2012

J. Am. Soc. Mass Spectrom.

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CV. Protein complexes in the gas phase: Technology for structural genomics and proteomics. Chem Rev 2007; 107: 3544. Cristoni S, Rubini S, Bernardi LR. Development and applications of surface-activated chemical ionization. Mass Spectrom Rev 2007; 26: 645. De Laeter JR, Hidaka H. The role of mass spectrometry to study the Oklo-Bangombe natural reactors. Mass Spectrom Rev 2007; 26: 683. Diaz-Cruz MS, Barcelo D. Recent advances in LC-MS residue analysis of veterinary medicines in the terrestrial environment. Trends Anal Chem 2007; 26: 637. Downard KM. Cavendish's crocodile and dark horse: The lives of Rutherford and Aston in parallel. Mass Spectrom Rev 2007; 26: 713. Gentili A. LC-MS methods for analyzing anti-inflammatory drugs in animal-food products. Trends Anal Chem 2007; 26: 595. Gingras AC, Gstaiger M, Raught B, Aebersold R. Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol 2007; 8: 645. Hao CY, Zhao XM, Yang P. GC-MS and HPLC-MS analysis of bioactive pharmaceuticals and personal-care products in environmental matrices. Trends Anal Chem 2007; 26: 569. Hardouin J. Protein sequence information by matrix-assisted laser desorption/ ionization in-source decay mass spectrometry. Mass Spectrom Rev 2007; 26: 672. Hernandez F, Sancho JV, Ibanez M, Guerrero C. Antibiotic residue determination in environmental waters by LC-MS. Trends Anal Chem 2007; 26: 466. Hernando MD, Gomez MJ, Aguera A, Fernandez-Alba AR. LC-MS analysis of basic pharmaceuticals (β-blockers and anti-ulcer agents) in wastewater and surface water. Trends Anal Chem 2007; 26: 581. Kanu AB, Dwivedi P, Tam M, Matz L, Hill HH. Special feature: Perspective: Ion mobility-mass spectrometry. J Mass Spectrom 2008; 43: 1. Kolakowski BM, Mester Z. Review of applications of high-field asymmetric waveform ion mobility spectrometry (FAIMS) and differential mobility spectrometry (DMS). Analyst 2007; 132: 842. Kool DM, Wrage N, Oenema O, Dolfing J, Van Groenigen JW. Oxygen exchange between (de)nitrification intermediates and H 2 O and its implications for source determination of NO 3 and N 2 O: A review. Rapid Commun Mass Spectrom 2007; 21: 3569. Lill JR, Ingle ES, Liu PS, Pham V, Sandoval WN. Microwave-assisted proteomics. Mass Spectrom Rev 2007; 26: 657. Liu T, Belov ME, Jaitly N, Qian WJ, Smith RD. Accurate mass measurements in proteomics. Chem Rev 2007; 107: 3621. Lubec G, Afjehi-Sadat L. Limitations and pitfalls in protein identification by mass spectrometry. Chem Rev 2007; 107: 3568. Perez S, Barcelo D. Application of advanced MS techniques to analysis and identification of human and microbial metabolites of pharmaceuticals in the aquatic environment. Trends Anal Chem 2007; 26: 494. Pizzolato TM, De Alda MJL, Barcelo D. LC-based analysis of drugs of abuse and their metabolites in urine. Trends Anal Chem 2007; 26: 609. 2 INSTRUMENTAL TECHNIQUES & METHODS Bajad S, Shulaev V. Highly-parallel metabolomics approaches using LC-MS 2 for pharmaceutical and environmental analysis. Trends Anal Chem 2007; 26: 625. Borner J, Buchinger S, Schomburg D...

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Efficient calculation of exact mass isotopic distributions

Cited by 35 publications

References 13 publications

A hierarchical algorithm for calculating the isotopic fine structures of molecules

A hierarchical algorithm for calculating the isotopic fine structures of molecules

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